Accurate marker-assisted selection for non-astringent persimmon using a CAPS marker to complement a SCAR marker

Persimmon is classified as either pollination-constant non-astringent (PCNA) or non-PCNA on the basis of the loss of astringency in fruit. PCNA trait of persimmon has attracted much research attention owing to its economical merit, as there is no cost in removing astringency. To efficiently develop new PCNA cultivars in crossbreeding, marker-assisted selection plays a crucial role. Here, we describe a cleaved amplified polymorphic sequence (CAPS) marker that can be used to select PCNA persimmon. A sequence-characterized amplified region (SCAR) marker used to screen for PCNA offspring is unsuitable for populations recently derived from two non-PCNA parents (‘Yoshidagosho’ and ‘Toyoichi’), resulting in the selection of non-PCNA offspring as PCNA. To detect specific polymorphisms for these non-PCNA offspring, we analyzed fragment sizes of SCAR marker products by capillary DNA sequencing. A slightly lower-molecular-weight fragment at 353 bp was specifically detected in non-PCNA offspring but not in PCNA offspring. We treated the SCAR marker products with the StuI restriction enzyme and demonstrated that the smaller 353-bp fragment corresponded to allele a^353-1, one of four previously identified sequence polymorphisms at the 353-bp peak, and a^353-1 is linked to non-PCNA trait. Comprehensive analysis of 130 germplasms by the CAPS marker, detecting the truncated fragment after StuI treatment, indicated the presence of a^353-1 in 38 non-PCNA cultivars. Our findings suggest the potential use of the CAPS marker for selecting PCNA offspring derived from these 38 non-PCNA cultivars.